Enhancement of the detection signal of fluorescence microscopy in highly diluted solutions is of great importance in chemical analysis, sensing, and bioassay applications. Surface nanodroplets with atto‐ to femto‐liter volumes are promising tools for sensitive online detection by integrating their extremely efficient nano‐extraction and optical advantages. In this paper, the development of novel basic units of nanodroplets‐in‐a‐microdroplet by simple solvent exchange is reported. The encapsulated nanodroplets are applied for ultrasensitive and online detection in fluorescence imaging. The biphasic nature of the droplet composite enables simultaneous extraction and enrichment of both hydrophobic and hydrophilic compounds. Furthermore, the desirable lensing effect of the curved surface of the nanodroplets enhances the collection of light emitted from the fluorophore extracted in the droplets by ≈60‐fold, allowing sensitive and quantitative analysis of the fluorophore using fluorescence microscopy. The results highlight the potential of encapsulated nanodroplets as a simple and innovative method of signal enhancement in chemical analysis. By integrating selective concentration, extraction, and sensitive detection, the encapsulated nanodroplets reported here may have broad applications in many chemical and biological matrices.